Citrus Sinensis ID: 017761

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360------
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKSSTPPKVSSSQPMLIGGSNRQFASHFPTNPEQLDYHFTW
cccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHcccccccccccccccccccccHHHHHHHHHHHHccEEEccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHcHHHHHHHHHcccccccccccccccccccccccccccccccccccccc
ccccccHHHccccccccccccccccccccEEccccccccccHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccHHHHHccccccccEEEEccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHcccHHHHHHHHccccccccccccccccccHccHccccccHHHccccccc
mttvldveklrlpsleahSNAVAAnrqwtyfgavgpsteenlgtslatetltSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtnTSMWAQLTERERAsiigdsviveaapeeeyseqqplnksadleptHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSvksgstsrrkrpsvqevdysdplrylrattsssrlltANEEMQLSAGIQDLLKLEGLREVlsercggsptFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVqksstppkvsssqpmliggsnrqfashfptnpeqldyhftw
mttvldveklrlpsleahsNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtNTSMWAQLTERERASIIGDSVIVEAAPeeeyseqqplnkSADLEPTHEELKLLEeqvsqsiavrsrrqterkARRTRaaekaaanvmsvksgstsrrkrpsvqevdysdplrylRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAaaagvdqrelRRRLNYGilckdkmitsNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKsstppkvsssqpmLIGGSNRQFAShfptnpeqldyhftw
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTsdeaviaaasaeavalaraavkvakdaalMVNHHNsakpkskpaisssaDTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSrrqterkarrtraaekaaaNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKSSTPPKVSSSQPMLIGGSNRQFASHFPTNPEQLDYHFTW
*******************NAVAANRQWTYFGAVGP*********LATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMV************************************I******************************************************************************************************************LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALL*******************************************
**T*LD*EKLRL**********************************************************************************************************************************************************************************************************RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVL*********FAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKSSTPPKVSSSQPMLIGGSNRQ******************
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHH******************TSMWAQLTERERASIIGDSVIVEAAP***********KSADLEPTHEELKLLEEQVSQS********************************************VDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV*************PMLIGGSNRQFASHFPTNPEQLDYHFTW
**TVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNH*****************TNTSMWAQLTERERASIIGDSVIVE********************************VSQSIAVRSRRQTERKARRT*****************************DYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKSSTPPKVSSSQPMLIGGSNRQFASHFPTNPEQLDYHFTW
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEVQKSSTPPKVSSSQPMLIGGSNRQFASHFPTNPEQLDYHFTW
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query366 2.2.26 [Sep-21-2011]
O22056 572 RNA polymerase sigma fact yes no 0.844 0.540 0.578 1e-78
Q9LD95 547 RNA polymerase sigma fact no no 0.415 0.277 0.385 6e-21
P26683 390 RNA polymerase sigma fact yes no 0.344 0.323 0.421 5e-18
P38023 399 RNA polymerase sigma fact yes no 0.292 0.268 0.457 3e-14
Q31QG5 320 RNA polymerase sigma fact no no 0.292 0.334 0.436 1e-12
Q31ME3 320 RNA polymerase sigma fact no no 0.256 0.293 0.414 2e-12
O24621 571 RNA polymerase sigma fact no no 0.234 0.150 0.372 3e-12
P52322 416 RNA polymerase sigma fact no no 0.292 0.257 0.315 2e-10
Q03065 332 RNA polymerase sigma-B fa no no 0.254 0.280 0.333 1e-08
O24629 502 RNA polymerase sigma fact no no 0.357 0.260 0.307 3e-07
>sp|O22056|SIGB_ARATH RNA polymerase sigma factor sigB OS=Arabidopsis thaliana GN=SIGB PE=2 SV=2 Back     alignment and function desciption
 Score =  293 bits (751), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 188/325 (57%), Positives = 234/325 (72%), Gaps = 16/325 (4%)

Query: 1   MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
           +T++LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL TSDEAV+ 
Sbjct: 49  LTSMLDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVV 108

Query: 60  AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
           AA+AEAVALARAAVKVAKDA L  N +N+        ++SS     S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGI 162

Query: 120 IG-----DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTE 173
           +G     D+ IV        S ++ +    DLE   +E   L E+  S S+AVRS RQTE
Sbjct: 163 LGHLAVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTE 219

Query: 174 RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEM 233
           RKARR +  EK A+ + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE 
Sbjct: 220 RKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEH 279

Query: 234 QLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITS 293
           +LSAGIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI S
Sbjct: 280 ELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKS 339

Query: 294 NIRLVISIAKNYQGAGMNLQDLVQD 318
           NIRLVISIAKNYQGAGMNLQDLVQ+
Sbjct: 340 NIRLVISIAKNYQGAGMNLQDLVQE 364
Required for the transition of plastids into chloroplasts by coordinating nuclear and chloroplastic genomes under light conditions. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Promotes the biosynthesis of plastid-encoded tRNAs (e.g. trnE-UUC and trnV-UAC).
Arabidopsis thaliana (taxid: 3702)
>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis thaliana GN=SIGF PE=1 SV=1 Back     alignment and function description
>sp|P26683|RPOD_NOSS1 RNA polymerase sigma factor RpoD OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rpoD PE=3 SV=1 Back     alignment and function description
>sp|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD1 PE=3 SV=2 Back     alignment and function description
>sp|Q31QG5|RPOD3_SYNE7 RNA polymerase sigma factor rpoD3 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD3 PE=3 SV=1 Back     alignment and function description
>sp|Q31ME3|RPOD2_SYNE7 RNA polymerase sigma factor rpoD2 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD2 PE=1 SV=1 Back     alignment and function description
>sp|O24621|SIGC_ARATH RNA polymerase sigma factor sigC OS=Arabidopsis thaliana GN=SIGC PE=2 SV=1 Back     alignment and function description
>sp|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa GN=rpoD1 PE=3 SV=1 Back     alignment and function description
>sp|Q03065|RPSB_NOSS1 RNA polymerase sigma-B factor OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=sigB PE=3 SV=1 Back     alignment and function description
>sp|O24629|SIGA_ARATH RNA polymerase sigma factor sigA OS=Arabidopsis thaliana GN=SIGA PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query366
255565968 569 RNA polymerase sigma factor rpoD1, putat 0.830 0.534 0.683 3e-97
224126061 567 predicted protein [Populus trichocarpa] 0.866 0.559 0.688 2e-90
449454538 580 PREDICTED: RNA polymerase sigma factor s 0.841 0.531 0.623 2e-90
224144900 564 predicted protein [Populus trichocarpa] 0.860 0.558 0.667 1e-89
296090195 575 unnamed protein product [Vitis vinifera] 0.866 0.551 0.702 7e-85
225436223 578 PREDICTED: RNA polymerase sigma factor r 0.866 0.548 0.702 9e-85
7363218 575 sigma factor 2 [Sinapis alba] 0.844 0.537 0.572 3e-79
297843640 572 hypothetical protein ARALYDRAFT_470915 [ 0.852 0.545 0.593 1e-78
15223259 572 RNApolymerase sigma subunit 2 [Arabidops 0.844 0.540 0.578 7e-77
356509511 558 PREDICTED: RNA polymerase sigma factor r 0.833 0.546 0.578 2e-76
>gi|255565968|ref|XP_002523972.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis] gi|223536699|gb|EEF38340.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis] Back     alignment and taxonomy information
 Score =  361 bits (926), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 216/316 (68%), Positives = 256/316 (81%), Gaps = 12/316 (3%)

Query: 4   VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 62
           VLD+EKLRLPS EA S+++A N  WTY            G++LATETL TSDEAVIAAA+
Sbjct: 59  VLDLEKLRLPSFEAPSDSIAPNSPWTY---------ATFGSTLATETLITSDEAVIAAAA 109

Query: 63  AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 122
           AEAVALARAAVKVAKDAAL+V +  SA+ +SK  ++S +  + S W Q TE ERA IIGD
Sbjct: 110 AEAVALARAAVKVAKDAALLVKNFPSAETESK--LTSPSTIDASRWPQFTETERARIIGD 167

Query: 123 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 182
           SV  E  P EE S Q  + +S  LE TH+EL+LL++Q+S+ IAVRSRRQTERKARR RA 
Sbjct: 168 SVATETGPREESSMQSSIKESDYLELTHKELELLQKQLSEGIAVRSRRQTERKARRARAV 227

Query: 183 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 242
           EKAA++V+SVK GSTS++KR S+QEVDYSDPLRYLR TTS+SRLLTA+EE++LSA IQDL
Sbjct: 228 EKAASSVVSVKPGSTSKKKRGSLQEVDYSDPLRYLRGTTSTSRLLTASEELELSAAIQDL 287

Query: 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302
           LKLE L+E L+ER GG PTFAQWAAAAGVDQR LR+R+N+G +CKDKMI SNIRLVISIA
Sbjct: 288 LKLERLQEELAERYGGQPTFAQWAAAAGVDQRTLRKRINHGTICKDKMIKSNIRLVISIA 347

Query: 303 KNYQGAGMNLQDLVQD 318
           KNYQGAGMNLQDLVQ+
Sbjct: 348 KNYQGAGMNLQDLVQE 363

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|224126061|ref|XP_002319746.1| predicted protein [Populus trichocarpa] gi|222858122|gb|EEE95669.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|449454538|ref|XP_004145011.1| PREDICTED: RNA polymerase sigma factor sigB-like [Cucumis sativus] gi|449473951|ref|XP_004154029.1| PREDICTED: RNA polymerase sigma factor sigB-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|224144900|ref|XP_002325455.1| predicted protein [Populus trichocarpa] gi|222862330|gb|EEE99836.1| predicted protein [Populus trichocarpa] Back     alignment and taxonomy information
>gi|296090195|emb|CBI40014.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|225436223|ref|XP_002273602.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Vitis vinifera] Back     alignment and taxonomy information
>gi|7363218|emb|CAB83106.1| sigma factor 2 [Sinapis alba] Back     alignment and taxonomy information
>gi|297843640|ref|XP_002889701.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp. lyrata] gi|297335543|gb|EFH65960.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|15223259|ref|NP_172330.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana] gi|75219074|sp|O22056.2|SIGB_ARATH RecName: Full=RNA polymerase sigma factor sigB; Short=Sigma factor B; Short=Sigma-B; AltName: Full=Protein ABERRANT CHLOROPLAST 1; AltName: Full=RNA polymerase sigma factor sig1; Short=Atsig1; Short=Sigma factor 1; AltName: Full=RNA polymerase sigma factor sig2; Short=Atsig2; Short=Sigma factor 2; AltName: Full=RNA polymerase sigma factor sigA; Short=Sigma factor A; Short=Sigma-A; Flags: Precursor gi|6664315|gb|AAF22897.1|AC006932_14 T27G7.22 [Arabidopsis thaliana] gi|9802550|gb|AAF99752.1|AC003981_2 F22O13.2 [Arabidopsis thaliana] gi|2443357|dbj|BAA22427.1| SigB [Arabidopsis thaliana] gi|2597831|emb|CAA75584.1| sigma factor [Arabidopsis thaliana] gi|2879922|dbj|BAA24825.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana] gi|5478446|dbj|BAA82449.1| sigma factor SigB [Arabidopsis thaliana] gi|133778838|gb|ABO38759.1| At1g08540 [Arabidopsis thaliana] gi|332190182|gb|AEE28303.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|356509511|ref|XP_003523491.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query366
TAIR|locus:2025650 572 SIG2 "AT1G08540" [Arabidopsis 0.855 0.547 0.464 4.1e-65
UNIPROTKB|Q84LK8 572 SIG6 "Sig6" [Oryza sativa Japo 0.508 0.325 0.310 2.6e-19
TAIR|locus:2057996 547 SIGF "AT2G36990" [Arabidopsis 0.330 0.221 0.401 4.9e-17
UNIPROTKB|O48655 519 rsigA "Plastid RNA polymerase 0.275 0.194 0.392 1.6e-10
TAIR|locus:2084420 571 SIGC "AT3G53920" [Arabidopsis 0.243 0.155 0.359 2.4e-10
TAIR|locus:2010871 502 SIGA "AT1G64860" [Arabidopsis 0.308 0.225 0.321 2.5e-06
TAIR|locus:2025650 SIG2 "AT1G08540" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
 Score = 663 (238.4 bits), Expect = 4.1e-65, P = 4.1e-65
 Identities = 149/321 (46%), Positives = 189/321 (58%)

Query:     1 MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTXXXXXXXX 60
             +T++LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL         
Sbjct:    49 LTSMLDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVV 108

Query:    61 XXXXXXXXXXXXXXXXXXXXXMVNHHNXXXXXXXXXXXXXXDTNTSMWAQLTERERASII 120
                                  +  + N                  S W Q TE+ERA I+
Sbjct:   109 AAAAEAVALARAAVKVAKDATLFKNSNNTNLLTSSTAD-----KRSKWDQFTEKERAGIL 163

Query:   121 GDSVIVEAAPEEEYSEQQPLNKSA--DLEPT-HEELKLLEEQVSQSIAVRSXXXXXXXXX 177
             G   + +     +       NK +  DLE    EE++LLEEQ S S+AVRS         
Sbjct:   164 GHLAVSDNGIVSDKITASASNKESIGDLESEKQEEVELLEEQPSVSLAVRSTRQTERKAR 223

Query:   178 XXXXXXXXXXNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 237
                        + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSA
Sbjct:   224 RAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSA 283

Query:   238 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 297
             GIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRL
Sbjct:   284 GIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRL 343

Query:   298 VISIAKNYQGAGMNLQDLVQD 318
             VISIAKNYQGAGMNLQDLVQ+
Sbjct:   344 VISIAKNYQGAGMNLQDLVQE 364
GO:0003677 "DNA binding" evidence=ISS
GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS
GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS
GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS
GO:0009507 "chloroplast" evidence=ISM;IDA
GO:0071482 "cellular response to light stimulus" evidence=IEP;IMP
GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA;TAS
GO:0009658 "chloroplast organization" evidence=IMP
GO:0006399 "tRNA metabolic process" evidence=IMP
GO:0001053 "plastid sigma factor activity" evidence=IMP
GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP
GO:0009637 "response to blue light" evidence=IGI;RCA
GO:0010114 "response to red light" evidence=IEP;RCA
GO:0006098 "pentose-phosphate shunt" evidence=RCA
GO:0006364 "rRNA processing" evidence=RCA
GO:0009902 "chloroplast relocation" evidence=RCA
GO:0010027 "thylakoid membrane organization" evidence=RCA
GO:0010218 "response to far red light" evidence=RCA
GO:0016117 "carotenoid biosynthetic process" evidence=RCA
GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA
GO:0034660 "ncRNA metabolic process" evidence=RCA
GO:0016987 "sigma factor activity" evidence=ISS
UNIPROTKB|Q84LK8 SIG6 "Sig6" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2057996 SIGF "AT2G36990" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|O48655 rsigA "Plastid RNA polymerase sigma factor" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
TAIR|locus:2084420 SIGC "AT3G53920" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
TAIR|locus:2010871 SIGA "AT1G64860" [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Your Input:
estExt_fgenesh4_pm.C_LG_XIII0293
hypothetical protein (568 aa)
(Populus trichocarpa)
Predicted Functional Partners:
eugene3.29520003
annotation not avaliable (742 aa)
    • • 0.499
fgenesh4_pm.C_LG_X000986
hypothetical protein (932 aa)
      • 0.472
gw1.XIV.2088.1
hypothetical protein (955 aa)
  ••  • 0.429
estExt_fgenesh4_pg.C_13160002
hypothetical protein (165 aa)
  •   • 0.415
estExt_Genewise1_v1.C_LG_X3691
SubName- Full=Putative uncharacterized protein; (165 aa)
  •   • 0.410
grail3.3134000101
Predicted protein (100 aa)
      • 0.406
eugene3.00020721
hypothetical protein (1053 aa)
  •     0.404

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query366
TIGR02997 298 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f 2e-24
PRK07406 373 PRK07406, PRK07406, RNA polymerase sigma factor Rp 4e-23
PRK07405 317 PRK07405, PRK07405, RNA polymerase sigma factor Si 2e-18
PRK05949 327 PRK05949, PRK05949, RNA polymerase sigma factor; V 7e-15
PRK05901 509 PRK05901, PRK05901, RNA polymerase sigma factor; P 1e-10
PRK07598 415 PRK07598, PRK07598, RNA polymerase sigma factor Si 1e-10
COG0568 342 COG0568, RpoD, DNA-directed RNA polymerase, sigma 6e-09
TIGR02393 238 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor 1e-07
PRK05658 619 PRK05658, PRK05658, RNA polymerase sigma factor Rp 8e-05
TIGR02394 285 TIGR02394, rpoS_proteo, RNA polymerase sigma facto 2e-04
PRK07921 324 PRK07921, PRK07921, RNA polymerase sigma factor Si 2e-04
PRK09210 367 PRK09210, PRK09210, RNA polymerase sigma factor Rp 4e-04
TIGR02392 270 TIGR02392, rpoH_proteo, alternative sigma factor R 5e-04
PRK06596 284 PRK06596, PRK06596, RNA polymerase factor sigma-32 0.002
>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information 
 Score =  100 bits (252), Expect = 2e-24
 Identities = 50/107 (46%), Positives = 71/107 (66%), Gaps = 2/107 (1%)

Query: 212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAG 270
           D +R YL+       LLT  EE++L+  +Q ++ LE LRE L E+ G  P+  +WAAAAG
Sbjct: 1   DLVRLYLQ-EIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAG 59

Query: 271 VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           + + ELR+RL  G   K+KMI +N+RLV+S+AK YQ  G+ L DL+Q
Sbjct: 60  LSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQ 106

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393). Length = 298
>gnl|CDD|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>gnl|CDD|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated Back     alignment and domain information
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional Back     alignment and domain information
>gnl|CDD|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated Back     alignment and domain information
>gnl|CDD|223642 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Back     alignment and domain information
>gnl|CDD|213709 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS Back     alignment and domain information
>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed Back     alignment and domain information
>gnl|CDD|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH Back     alignment and domain information
>gnl|CDD|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 366
PRK07598 415 RNA polymerase sigma factor SigC; Validated 100.0
TIGR02997 298 Sig70-cyanoRpoD RNA polymerase sigma factor, cyano 100.0
PRK07406 373 RNA polymerase sigma factor RpoD; Validated 100.0
PRK05949 327 RNA polymerase sigma factor; Validated 100.0
PRK07405 317 RNA polymerase sigma factor SigD; Validated 100.0
PRK05901 509 RNA polymerase sigma factor; Provisional 99.98
COG0568 342 RpoD DNA-directed RNA polymerase, sigma subunit (s 99.98
PRK07921 324 RNA polymerase sigma factor SigB; Reviewed 99.95
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 99.91
PRK09210 367 RNA polymerase sigma factor RpoD; Validated 99.91
TIGR02392 270 rpoH_proteo alternative sigma factor RpoH. A sigma 99.86
PRK06596 284 RNA polymerase factor sigma-32; Reviewed 99.86
PRK07122 264 RNA polymerase sigma factor SigF; Reviewed 99.85
PRK07500 289 rpoH2 RNA polymerase factor sigma-32; Reviewed 99.83
TIGR02393 238 RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter 99.78
PRK05657 325 RNA polymerase sigma factor RpoS; Validated 99.74
PRK07408 256 RNA polymerase sigma factor SigF; Reviewed 99.71
TIGR02394 285 rpoS_proteo RNA polymerase sigma factor RpoS. A si 99.67
COG1191 247 FliA DNA-directed RNA polymerase specialized sigma 99.63
TIGR02850 254 spore_sigG RNA polymerase sigma-G factor. Members 99.6
PRK05911 257 RNA polymerase sigma factor sigma-28; Reviewed 99.58
PRK08215 258 sporulation sigma factor SigG; Reviewed 99.57
PRK06288 268 RNA polymerase sigma factor WhiG; Reviewed 99.45
TIGR02980 227 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G 99.42
TIGR02941 255 Sigma_B RNA polymerase sigma-B factor. This sigma 99.41
PRK08583 257 RNA polymerase sigma factor SigB; Validated 99.36
TIGR02885 231 spore_sigF RNA polymerase sigma-F factor. Members 99.3
PRK12427 231 flagellar biosynthesis sigma factor; Provisional 99.25
PRK05803233 sporulation sigma factor SigK; Reviewed 99.2
TIGR02895 218 spore_sigI RNA polymerase sigma-I factor. Members 99.18
PRK05572 252 sporulation sigma factor SigF; Validated 99.15
TIGR02479 224 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f 99.11
PRK06986 236 fliA flagellar biosynthesis sigma factor; Validate 99.09
PRK07670 251 RNA polymerase sigma factor SigD; Validated 99.08
PRK08301234 sporulation sigma factor SigE; Reviewed 98.63
TIGR02846227 spore_sigmaK RNA polymerase sigma-K factor. The sp 98.63
PF0454271 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762 98.52
TIGR02835234 spore_sigmaE RNA polymerase sigma-E factor. Member 98.46
TIGR02937158 sigma70-ECF RNA polymerase sigma factor, sigma-70 98.23
PRK08311 237 putative RNA polymerase sigma factor SigI; Reviewe 98.16
PF0014037 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr 98.13
PRK08295208 RNA polymerase factor sigma-70; Validated 98.06
PRK09652182 RNA polymerase sigma factor RpoE; Provisional 98.0
PRK11922 231 RNA polymerase sigma factor; Provisional 97.96
TIGR02859198 spore_sigH RNA polymerase sigma-H factor. Members 97.93
PRK05602186 RNA polymerase sigma factor; Reviewed 97.87
PRK12513194 RNA polymerase sigma factor; Provisional 97.86
PRK09641187 RNA polymerase sigma factor SigW; Provisional 97.8
PRK09648189 RNA polymerase sigma factor SigD; Reviewed 97.75
TIGR02948187 SigW_bacill RNA polymerase sigma-W factor. This si 97.71
PRK09640188 RNA polymerase sigma factor SigX; Reviewed 97.69
PRK13919186 putative RNA polymerase sigma E protein; Provision 97.55
PRK09638176 RNA polymerase sigma factor SigY; Reviewed 97.51
PRK12519194 RNA polymerase sigma factor; Provisional 97.5
PRK11923193 algU RNA polymerase sigma factor AlgU; Provisional 97.45
PRK06811189 RNA polymerase factor sigma-70; Validated 97.45
TIGR02939190 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s 97.43
PRK09646194 RNA polymerase sigma factor SigK; Reviewed 97.36
PRK06759154 RNA polymerase factor sigma-70; Validated 97.36
TIGR02954169 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02 97.32
PRK11924179 RNA polymerase sigma factor; Provisional 97.27
PRK12514179 RNA polymerase sigma factor; Provisional 97.26
PRK05658 619 RNA polymerase sigma factor RpoD; Validated 97.22
TIGR02989159 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop 97.22
TIGR02985161 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba 97.14
PRK12512184 RNA polymerase sigma factor; Provisional 97.06
PRK12534187 RNA polymerase sigma factor; Provisional 97.04
TIGR02952170 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02 96.99
PRK12536181 RNA polymerase sigma factor; Provisional 96.92
PRK09643192 RNA polymerase sigma factor SigM; Reviewed 96.89
PRK12524196 RNA polymerase sigma factor; Provisional 96.86
PRK12522173 RNA polymerase sigma factor; Provisional 96.82
PRK12531194 RNA polymerase sigma factor; Provisional 96.78
PRK12539184 RNA polymerase sigma factor; Provisional 96.78
PRK12526206 RNA polymerase sigma factor; Provisional 96.77
PRK12537182 RNA polymerase sigma factor; Provisional 96.71
TIGR02984189 Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl 96.65
PRK12515189 RNA polymerase sigma factor; Provisional 96.62
PRK12538233 RNA polymerase sigma factor; Provisional 96.5
PRK12518175 RNA polymerase sigma factor; Provisional 96.45
PRK09639166 RNA polymerase sigma factor SigX; Provisional 96.33
PRK12543179 RNA polymerase sigma factor; Provisional 96.11
PF0453978 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 96.0
PRK09415179 RNA polymerase factor sigma C; Reviewed 95.99
COG1595182 RpoE DNA-directed RNA polymerase specialized sigma 95.9
TIGR02983162 SigE-fam_strep RNA polymerase sigma-70 factor, sig 95.72
PRK09647203 RNA polymerase sigma factor SigE; Reviewed 95.25
PRK12547164 RNA polymerase sigma factor; Provisional 95.01
PRK12541161 RNA polymerase sigma factor; Provisional 94.76
PRK12532 195 RNA polymerase sigma factor; Provisional 94.75
TIGR02999183 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f 94.74
TIGR03001 244 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco 94.72
TIGR02947193 SigH_actino RNA polymerase sigma-70 factor, TIGR02 94.68
PRK08241 339 RNA polymerase factor sigma-70; Validated 94.62
TIGR02943 188 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02 94.56
PRK12520 191 RNA polymerase sigma factor; Provisional 94.53
PRK09644165 RNA polymerase sigma factor SigM; Provisional 94.22
PRK12542185 RNA polymerase sigma factor; Provisional 94.18
PRK12516187 RNA polymerase sigma factor; Provisional 94.15
PRK09637181 RNA polymerase sigma factor SigZ; Provisional 94.14
PRK09649185 RNA polymerase sigma factor SigC; Reviewed 94.07
PRK12544 206 RNA polymerase sigma factor; Provisional 93.93
PRK12528161 RNA polymerase sigma factor; Provisional 93.91
PRK09645173 RNA polymerase sigma factor SigL; Provisional 93.79
TIGR02959170 SigZ RNA polymerase sigma factor, SigZ family. Thi 93.65
TIGR02960 324 SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa 93.59
PRK12533 216 RNA polymerase sigma factor; Provisional 93.46
PRK12523172 RNA polymerase sigma factor; Reviewed 93.46
PRK12546188 RNA polymerase sigma factor; Provisional 93.13
TIGR02950154 SigM_subfam RNA polymerase sigma factor, SigM fami 92.89
PRK07037163 extracytoplasmic-function sigma-70 factor; Validat 92.76
PRK12530189 RNA polymerase sigma factor; Provisional 92.4
PRK09651172 RNA polymerase sigma factor FecI; Provisional 92.22
PRK12540182 RNA polymerase sigma factor; Provisional 91.99
PRK09642160 RNA polymerase sigma factor SigW; Reviewed 91.91
PRK12517188 RNA polymerase sigma factor; Provisional 91.89
PRK12535196 RNA polymerase sigma factor; Provisional 91.39
PRK12545 201 RNA polymerase sigma factor; Provisional 91.08
PRK12525168 RNA polymerase sigma factor; Provisional 87.16
PRK12511182 RNA polymerase sigma factor; Provisional 86.67
PRK12527159 RNA polymerase sigma factor; Reviewed 86.67
TIGR02957 281 SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa 86.63
PRK09636 293 RNA polymerase sigma factor SigJ; Provisional 86.11
PRK12529178 RNA polymerase sigma factor; Provisional 84.15
PRK06704 228 RNA polymerase factor sigma-70; Validated 84.01
COG0568 342 RpoD DNA-directed RNA polymerase, sigma subunit (s 82.5
>PRK07598 RNA polymerase sigma factor SigC; Validated Back     alignment and domain information 
Probab=100.00  E-value=1.8e-38  Score=319.92  Aligned_cols=155  Identities=33%  Similarity=0.476  Sum_probs=143.3

Q ss_pred             CCCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhcCCCCchHHHH
Q 017761          208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWA  266 (366)
Q Consensus       208 ~~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~--------------------le~~r~~L~~~~GrePT~~eWA  266 (366)
                      ..+.||++ ||++| |+++|||++||++|+++||++++                    |++++.+|++++|++||..|||
T Consensus        56 ~~~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa  134 (415)
T PRK07598         56 RRSTDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWA  134 (415)
T ss_pred             CCCCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            34589999 99999 99999999999999999999999                    8999999999999999999999


Q ss_pred             HHhcCCHHHHHHh----------------------hhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHH
Q 017761          267 AAAGVDQRELRRR----------------------LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLE  324 (366)
Q Consensus       267 ~aag~~~~~L~~~----------------------L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi  324 (366)
                      .++|+++.+|+.+                      ++.|+.|+++||++|+|||++||++|.++|++++||||||+|||+
T Consensus       135 ~~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~  214 (415)
T PRK07598        135 KTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLE  214 (415)
T ss_pred             HHhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence            7777666666555                      567889999999999999999999999999999999999999999


Q ss_pred             h--ccCCC--CCCccccHH-HHHHHHHHHHHhcCCCCCCCcCcccc
Q 017761          325 V--QKSST--PPKVSSSQP-MLIGGSNRQFASHFPTNPEQLDYHFT  365 (366)
Q Consensus       325 ~--ekFD~--G~rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~~~  365 (366)
                      +  ++|||  |++||||+. |||++|.|+|++++|+|+  ||.|++
T Consensus       215 ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIr--lP~~i~  258 (415)
T PRK07598        215 RAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIR--LPVHIT  258 (415)
T ss_pred             HHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCcee--hhHHHH
Confidence            5  89999  999999987 599999999999999999  999974

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family Back     alignment and domain information
>PRK07406 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK05949 RNA polymerase sigma factor; Validated Back     alignment and domain information
>PRK07405 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>PRK05901 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Back     alignment and domain information
>PRK07921 RNA polymerase sigma factor SigB; Reviewed Back     alignment and domain information
>PRK05658 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>PRK09210 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>TIGR02392 rpoH_proteo alternative sigma factor RpoH Back     alignment and domain information
>PRK06596 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>PRK07122 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed Back     alignment and domain information
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain Back     alignment and domain information
>PRK05657 RNA polymerase sigma factor RpoS; Validated Back     alignment and domain information
>PRK07408 RNA polymerase sigma factor SigF; Reviewed Back     alignment and domain information
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS Back     alignment and domain information
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] Back     alignment and domain information
>TIGR02850 spore_sigG RNA polymerase sigma-G factor Back     alignment and domain information
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed Back     alignment and domain information
>PRK08215 sporulation sigma factor SigG; Reviewed Back     alignment and domain information
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed Back     alignment and domain information
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily Back     alignment and domain information
>TIGR02941 Sigma_B RNA polymerase sigma-B factor Back     alignment and domain information
>PRK08583 RNA polymerase sigma factor SigB; Validated Back     alignment and domain information
>TIGR02885 spore_sigF RNA polymerase sigma-F factor Back     alignment and domain information
>PRK12427 flagellar biosynthesis sigma factor; Provisional Back     alignment and domain information
>PRK05803 sporulation sigma factor SigK; Reviewed Back     alignment and domain information
>TIGR02895 spore_sigI RNA polymerase sigma-I factor Back     alignment and domain information
>PRK05572 sporulation sigma factor SigF; Validated Back     alignment and domain information
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family Back     alignment and domain information
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated Back     alignment and domain information
>PRK07670 RNA polymerase sigma factor SigD; Validated Back     alignment and domain information
>PRK08301 sporulation sigma factor SigE; Reviewed Back     alignment and domain information
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor Back     alignment and domain information
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor Back     alignment and domain information
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family Back     alignment and domain information
>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed Back     alignment and domain information
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1 Back     alignment and domain information
>PRK08295 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>PRK09652 RNA polymerase sigma factor RpoE; Provisional Back     alignment and domain information
>PRK11922 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02859 spore_sigH RNA polymerase sigma-H factor Back     alignment and domain information
>PRK05602 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PRK12513 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09641 RNA polymerase sigma factor SigW; Provisional Back     alignment and domain information
>PRK09648 RNA polymerase sigma factor SigD; Reviewed Back     alignment and domain information
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor Back     alignment and domain information
>PRK09640 RNA polymerase sigma factor SigX; Reviewed Back     alignment and domain information
>PRK13919 putative RNA polymerase sigma E protein; Provisional Back     alignment and domain information
>PRK09638 RNA polymerase sigma factor SigY; Reviewed Back     alignment and domain information
>PRK12519 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional Back     alignment and domain information
>PRK06811 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE Back     alignment and domain information
>PRK09646 RNA polymerase sigma factor SigK; Reviewed Back     alignment and domain information
>PRK06759 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family Back     alignment and domain information
>PRK11924 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12514 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK05658 RNA polymerase sigma factor RpoD; Validated Back     alignment and domain information
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family Back     alignment and domain information
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1 Back     alignment and domain information
>PRK12512 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12534 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family Back     alignment and domain information
>PRK12536 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09643 RNA polymerase sigma factor SigM; Reviewed Back     alignment and domain information
>PRK12524 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12522 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12531 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12539 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12526 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12537 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1 Back     alignment and domain information
>PRK12515 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12538 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12518 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09639 RNA polymerase sigma factor SigX; Provisional Back     alignment and domain information
>PRK12543 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription Back     alignment and domain information
>PRK09415 RNA polymerase factor sigma C; Reviewed Back     alignment and domain information
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription] Back     alignment and domain information
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family Back     alignment and domain information
>PRK09647 RNA polymerase sigma factor SigE; Reviewed Back     alignment and domain information
>PRK12547 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12541 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12532 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family Back     alignment and domain information
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1 Back     alignment and domain information
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family Back     alignment and domain information
>PRK08241 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family Back     alignment and domain information
>PRK12520 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09644 RNA polymerase sigma factor SigM; Provisional Back     alignment and domain information
>PRK12542 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12516 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09637 RNA polymerase sigma factor SigZ; Provisional Back     alignment and domain information
>PRK09649 RNA polymerase sigma factor SigC; Reviewed Back     alignment and domain information
>PRK12544 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12528 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09645 RNA polymerase sigma factor SigL; Provisional Back     alignment and domain information
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family Back     alignment and domain information
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family Back     alignment and domain information
>PRK12533 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12523 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>PRK12546 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family Back     alignment and domain information
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated Back     alignment and domain information
>PRK12530 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09651 RNA polymerase sigma factor FecI; Provisional Back     alignment and domain information
>PRK12540 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK09642 RNA polymerase sigma factor SigW; Reviewed Back     alignment and domain information
>PRK12517 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12535 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12545 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12525 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12511 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK12527 RNA polymerase sigma factor; Reviewed Back     alignment and domain information
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family Back     alignment and domain information
>PRK09636 RNA polymerase sigma factor SigJ; Provisional Back     alignment and domain information
>PRK12529 RNA polymerase sigma factor; Provisional Back     alignment and domain information
>PRK06704 RNA polymerase factor sigma-70; Validated Back     alignment and domain information
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query366
1l9u_H 332 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 1e-06
1l9z_H 438 Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun 7e-06
3ugo_A245 Crystal Structure Of Rna-Polymerase Sigma Subunit D 2e-05
1ku2_A241 Crystal Structure Of Thermus Aquaticus Rna Polymera 3e-05
3les_A179 2f5 Epitope Scaffold Es2 Length = 179 3e-04
>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332 Back     alignment and structure 
Iteration: 1

 Score = 51.2 bits (121), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 38/123 (30%), Positives = 61/123 (49%), Gaps = 15/123 (12%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 259 SPTFAQWAAAAGVDQRELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDL 315
           +    +         +EL+R L+    G   +  +I +N+RLV+SIAK Y G G++  DL
Sbjct: 62  TARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL 121
Query: 316 VQD 318
           +Q+
Sbjct: 122 IQE 124
>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438 Back     alignment and structure
>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2 Complexed With -10 Promoter Element Ssdna Oligo (Tacaat) Length = 245 Back     alignment and structure
>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase Sigma Subunit Fragment Containing Regions 1.2 To 3.1 Length = 241 Back     alignment and structure
>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query366
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 2e-08
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 6e-08
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 6e-08
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 2e-06
1l0o_C 243 Sigma factor; bergerat fold, helix-turn-helix, pro 4e-06
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 2e-04
1vt4_I 1221 APAF-1 related killer DARK; drosophila apoptosome, 4e-04
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Length = 423 Back     alignment and structure
 Score = 54.1 bits (130), Expect = 2e-08
 Identities = 34/199 (17%), Positives = 63/199 (31%), Gaps = 20/199 (10%)

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVR-SRRQTERKARR 178
             D  + +     E        +   L+   EE  L   ++S S  VR    +  +    
Sbjct: 35  EPDPDLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLL 94

Query: 179 TRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAG 238
           T   E   A  +     +  +    +  + D                ++ A         
Sbjct: 95  TLEEEVELARKVEEGMEAIKKLSEITGLDPDLIR------------EVVRAKILGSARVR 142

Query: 239 IQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLV 298
               LK     + + E      +  +       + +        G   +  +I +N+RLV
Sbjct: 143 HIPGLKETLDPKTVEEIDQKLKSLPK-------EHKRYLHIAREGEAARQHLIEANLRLV 195

Query: 299 ISIAKNYQGAGMNLQDLVQ 317
           +SIAK Y G G++  DL+Q
Sbjct: 196 VSIAKKYTGRGLSFLDLIQ 214
>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 1ku2_A 3lev_A* 3les_A* Length = 245 Back     alignment and structure
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Length = 438 Back     alignment and structure
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Length = 339 Back     alignment and structure
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2 Length = 243 Back     alignment and structure
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 613 Back     alignment and structure
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query366
1l9z_H 438 Sigma factor SIGA; helix-turn-helix, coiled-coil, 99.95
2a6h_F 423 RNA polymerase sigma factor RPOD; RNA polymerase h 99.95
3ugo_A245 RNA polymerase sigma factor; protein-DNA complex, 99.95
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 99.45
1sig_A339 Sigma70, RNA polymerase primary sigma factor; RNA 99.42
1rp3_A 239 RNA polymerase sigma factor sigma-28 (FLIA); trans 98.72
1l0o_C 243 Sigma factor; bergerat fold, helix-turn-helix, pro 98.68
1or7_A194 Sigma-24, RNA polymerase sigma-E factor; regulatio 97.99
2q1z_A184 RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc 97.6
3mzy_A 164 RNA polymerase sigma-H factor; PSI, MCSG, structur 97.07
2o7g_A112 Probable RNA polymerase sigma-C factor; sigma fact 96.96
1h3l_A87 RNA polymerase sigma factor; transcription, DNA-bi 96.86
3iyd_F 613 RNA polymerase sigma factor RPOD; transcription, i 95.72
2lfw_A157 PHYR sigma-like domain; signal transduction, respo 94.69
3n0r_A 286 Response regulator; sigma factor, receiver, two-co 86.25
>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Back     alignment and structure
Probab=99.95  E-value=1.8e-28  Score=247.55  Aligned_cols=154  Identities=26%  Similarity=0.322  Sum_probs=132.1

Q ss_pred             CCCCChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHH------------------HHhhcCCCCchHHHHHH
Q 017761          208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREV------------------LSERCGGSPTFAQWAAA  268 (366)
Q Consensus       208 ~~~~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~------------------L~~~~GrePT~~eWA~a  268 (366)
                      ..+.|+++ ||++| +++||||++||++|+++|+.++.++.....                  .....++.|+..+|+..
T Consensus        90 ~~~~d~~~~Yl~ei-~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  168 (438)
T 1l9z_H           90 VSTSDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDP  168 (438)
T ss_pred             CCCCChHHHHHHHh-ccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccc
Confidence            34578999 99999 999999999999999999998654432221                  22345688998887532


Q ss_pred             ------------hcCCHHHHHHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CC
Q 017761          269 ------------AGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PP  332 (366)
Q Consensus       269 ------------ag~~~~~L~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~  332 (366)
                                  .+++..+|...+..|..|+++||.+|+|+|++||++|.|+|++++||||||+||||+  ++||+  |+
T Consensus       169 ~~~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~  248 (438)
T 1l9z_H          169 KTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRF  248 (438)
T ss_pred             hhhhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCC
Confidence                        355667888888889999999999999999999999999999999999999999994  89999  89


Q ss_pred             CccccHH-HHHHHHHHHHHhcCCCCCCCcCccc
Q 017761          333 KVSSSQP-MLIGGSNRQFASHFPTNPEQLDYHF  364 (366)
Q Consensus       333 rFSTYA~-wIr~~I~R~i~d~~~~V~~~l~~~~  364 (366)
                      +|+||+. ||++.|.++|++++++|+  +|+|.
T Consensus       249 rFsTYA~~wIR~~I~~~i~~~~R~ir--lp~~~  279 (438)
T 1l9z_H          249 KFSTYATWWIRQAINRAIADQARTIR--IPVHM  279 (438)
T ss_pred             ChHHHHHHHHHHHHHHHHHHhcchhc--cchHH
Confidence            9999986 599999999999999998  88885
>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Back     alignment and structure
>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A* Back     alignment and structure
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Back     alignment and structure
>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Back     alignment and structure
>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Back     alignment and structure
>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2 Back     alignment and structure
>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A Back     alignment and structure
>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Back     alignment and structure
>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis} Back     alignment and structure
>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1 Back     alignment and structure
>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Back     alignment and structure
>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP} Back     alignment and structure
>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 366
d1ku2a2180 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq 2e-06
d1siga_334 a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5 4e-06
d1rp3a387 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A 6e-04
>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 180 Back     information, alignment and structure

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score = 45.6 bits (107), Expect = 2e-06
 Identities = 31/140 (22%), Positives = 56/140 (40%), Gaps = 32/140 (22%)

Query: 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK------------------LEGLREV 251
           SDP+R YL        LLT  EE+ L+  +++ ++                  +   + +
Sbjct: 1   SDPVRQYLH-EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKIL 59

Query: 252 LSERCGGSPTFAQWAAAAGVDQ------------RELRRRLNYGILCKDKMITSNIRLVI 299
            + R    P   +      V++            +        G   +  +I +N+RLV+
Sbjct: 60  GTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVV 119

Query: 300 SIAKNYQGAGMNLQDLVQDV 319
           SIAK Y G G++  DL+Q+ 
Sbjct: 120 SIAKKYTGRGLSFLDLIQEG 139
>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334 Back     information, alignment and structure
>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 87 Back     information, alignment and structure

Homologous Domains Detected by HHsearch ?

Original result of HHsearch against SCOP70(version1.75) database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query366
d1ku2a2180 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 100.0
d1siga_334 Sigma70 {Escherichia coli [TaxId: 562]} 99.89
d1rp3a387 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 99.71
d1or7a2113 SigmaE factor (RpoE) {Escherichia coli [TaxId: 562 97.79
d1l0oc_57 SigmaF {Bacillus stearothermophilus [TaxId: 1422]} 96.85
d1rp3a177 Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta 96.4
d1ku2a160 Sigma factor SigA {Thermus aquaticus [TaxId: 271]} 95.24
d1h3la_75 Sigma factor SigR {Streptomyces coelicolor a3(2) [ 94.03
>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure
class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=100.00  E-value=1.1e-36  Score=268.39  Aligned_cols=144  Identities=27%  Similarity=0.351  Sum_probs=119.7

Q ss_pred             CChhH-HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------------hhcCCCCchHHHHHHhcC
Q 017761          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLS------------------ERCGGSPTFAQWAAAAGV  271 (366)
Q Consensus       211 ~D~l~-YLkei~~~~~LLt~eEE~eLa~~Iq~l~~le~~r~~L~------------------~~~GrePT~~eWA~aag~  271 (366)
                      +|||+ ||++| |++||||++||++|+++|+.++.+.+...+..                  ...+..|...+|......
T Consensus         1 tDpVr~YLrei-g~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~   79 (180)
T d1ku2a2           1 SDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTV   79 (180)
T ss_dssp             CHHHHHHHHHH-TTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTH
T ss_pred             CCcHHHHHHHh-cCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHH
Confidence            58999 99999 99999999999999999998876554433221                  123445555554433222


Q ss_pred             ------------CHHHHHHhhhhhHHHHHHHHHHcHHHHHHHHHHcccCCCChhhHHHHhHHHHHh--ccCCC--CCCcc
Q 017761          272 ------------DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQDVEALLEV--QKSST--PPKVS  335 (366)
Q Consensus       272 ------------~~~~L~~~L~~G~~AR~kLI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLi~--ekFD~--G~rFS  335 (366)
                                  ..+.+...+..|..||++||.+|+|||++||++|.++|++|+||||||+||||+  ++|||  |++||
T Consensus        80 ~~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f~  159 (180)
T d1ku2a2          80 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS  159 (180)
T ss_dssp             HHHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCHH
Confidence                        235567788899999999999999999999999999999999999999999994  89999  99999


Q ss_pred             ccHHH-HHHHHHHHHHhcCCC
Q 017761          336 SSQPM-LIGGSNRQFASHFPT  355 (366)
Q Consensus       336 TYA~w-Ir~~I~R~i~d~~~~  355 (366)
                      |||+| |+++|.|+|+|++||
T Consensus       160 tya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         160 TYATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHHhCCC
Confidence            99875 999999999999987
>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Back     information, alignment and structure
>d1h3la_ a.177.1.1 (A:) Sigma factor SigR {Streptomyces coelicolor a3(2) [TaxId: 100226]} Back     information, alignment and structure